Finished successful USA -> JPN emuNAND conversion with working eShop access (no 007-2001 error). Tested and completed using AuReiNand 4.0.1
Rough Steps
Heads up: Install FBI as a separate install. If all you got is a H&S injected copy then use that to do this. You will lose the injected one later on during the conversion. You can reinject it if you want but it will be easier this way.
1) Downgrade your emuNAND to 9.1.0J using that mis-labeled downgrade pack... (it's tagged 9.2.0J)
2) Using GodMode9 inject SecureInfo_C into CTRNAND/rw/sys/ (same place where SecureInfo_A is at). This file does not replace your SecureInfo_A at all so yes both files will be present. I won't say how to make the SecureInfo_C file. There is information on gbatemp and 3dbrew.org
Note: At this point when you reboot you should get a Japanese UI and see plenty of duplicate icons. This is ok for now. You have both the normal region and Japanese region titles installed for may of the sys apps. Beware of the instability we will be working through.
3) Run Downgrade Check (
https://github.com/svanheulen/downgrade_check/releases) to get a list of extra/missing titles. Ignore any mismatch version alerts. Those will get self-resolved later. It is suggested at this point to grab the report it generates. You can either power down and copy the file from the SD card or use FTP to transfer it.
4) Use 3DNUS to download the missing titles. I know there is some. At the very least the JPN eula title is missing from the downgrade pack (well it isn't intended for region conversions...)
5) Use FBI to remove any extra titles and install any missing ones.
6) Reboot then run the Downgrade Check app again. This time it should only have version mis-match alerts. If there are still any extra or missing titles handle them now. Do this until it only gives you mis-match versions.
-----
Backup your Emunand here using EmuNAND9 please. This will give us a way to fix things up if the setup goes south during the next step -----
7) Use TinyFormat to quick format the system. Setup the unit again. The whole setup is in Japanese now. This part is important as it will location set the unit to somewhere in Japan. You can leave the location (first entry when you set your DOB) to the first one. Pretty sure that is Japan in a generic sense.
Note: If it crashes right when it hits the 3rd part then the eula package was missing... Restore your backup and make sure to install package 0004009B00013202
8) Use System Settings and upgrade to 10.7J
Congrats! You are all done. Now when you access eShop it should let you in. If you kept sysnand with no NNID linked you should be able to access the USA eShop from sysnand and the JPN eShop in emuNAND.
EDIT: Spoke too soon... I get 011-6949 when attempting to actually download anything since it seems to force a NNID link. :/